Plotting chord-diagram with R

Michael Nostalgie

2018-11-09

Chord diagram

A graphical method of displaying the inter-relationships between data in a matrix.
The data are arranged radially around a circle with the relationships between the data points typically drawn as arcs connecting the data.

circlize - a R package for circular visualization

Intro

Coordinate transformation

Data coordinate systems
Polar coordinate systems
Canvas coordinate systems

Layout

Rules of using circlize to make circular plot

How to use circlize?

circos.initialize(factors, xlim)

circos.track(factors, ylim)

for(sector.index in all.sector.index) {
    circos.points(x1, y1, sector.index)
    circos.lines(x2, y2, sector.index)
}

...

An example

Step 1 - Generate random data

set.seed(999)
n = 1000
df = data.frame(factors = sample(letters[1:8], n, replace = TRUE),
    x = rnorm(n), y = runif(n))
dplyr::tbl_df(df)

## # A tibble: 1,000 x 3
##    factors        x      y
##    <fct>      <dbl>  <dbl>
##  1 d       -0.338   0.228 
##  2 e        0.201   0.835 
##  3 a        0.603   0.651 
##  4 g       -0.225   0.861 
##  5 g       -0.0101  0.362 
##  6 a       -0.194   0.525 
##  7 e        0.00919 0.780 
##  8 a        1.44    0.674 
##  9 d        0.175   0.0761
## 10 e        0.472   0.969 
## # ... with 990 more rows

Step 2 - Initialize a circular layout

suppressMessages(library(circlize))
circos.par("track.height" = 0.1)
circos.initialize(factors = df$factors, x = df$x)

Step 3 - Add a track and drawing plot

circos.track(factors = df$factors, y = df$y,
    panel.fun = function(x, y) {
        circos.text(CELL_META$xcenter, CELL_META$cell.ylim[2] + uy(5, "mm"), CELL_META$sector.index)
        circos.axis(labels.cex = 0.6)
})
col = rep(c("#FF0000", "#00FF00"), 4)
circos.trackPoints(df$factors, df$x, df$y, col = col, pch = 16, cex = 0.5)
circos.text(-1, 0.5, "text", sector.index = "a", track.index = 1)

Step 4 - Add a track and drawing plot

bgcol = rep(c("#EFEFEF", "#CCCCCC"), 4)
circos.trackHist(df$factors, df$x, bin.size = 0.2, bg.col = bgcol, col = NA)

Plotting chord-diagram with R

Michael Nostalgie

2018-11-09

Chord diagram

circlize - a R package for circular visualization

Intro

Coordinate transformation

Layout

Rules of using circlize to make circular plot

How to use circlize?

An example

Step 1 - Generate random data

Step 2 - Initialize a circular layout

Step 3 - Add a track and drawing plot

Step 4 - Add a track and drawing plot

Repeat Step 3 / Step 4

More about using circlize to visualize your data

Linking genomic regions

Representation of transcript isoforms

Nested zooming

Resources

Thank you!